Variant report

Variant	rs11734947
Chromosome Location	chr4:7696171-7696172
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10937855	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735713	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1557818	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2057723	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs2057725	1.00[JPT][hapmap]
rs35787985	0.96[ASN][1000 genomes]
rs4286515	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57867692	0.91[ASN][1000 genomes]
rs6848579	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs757255	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886376	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs886378	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs929264	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs929265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv34156	chr4:7526515-7750588	Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv508272	chr4:7591967-7722112	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv878571	chr4:7637297-7743283	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv432557	chr4:7672785-7719249	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv432559	chr4:7680536-7719249	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv432563	chr4:7683417-7717629	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv432564	chr4:7683417-7719249	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv878572	chr4:7693469-7730392	Enhancers Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11734947	JAKMIP1	cis	parietal	SCAN
rs11734947	LOC93622	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7679800-7715600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:7685600-7707000	Weak transcription	Fetal Intestine Small	intestine
3	chr4:7686000-7698600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:7686200-7721000	Weak transcription	Brain Anterior Caudate	brain
5	chr4:7687000-7698000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:7688600-7696200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:7691600-7705400	Weak transcription	Brain Substantia Nigra	brain
8	chr4:7691600-7716200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:7693000-7698200	Weak transcription	Gastric	stomach
10	chr4:7693200-7699400	Weak transcription	Spleen	Spleen
11	chr4:7694000-7712600	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:7694200-7712600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:7694400-7699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:7695000-7696800	Enhancers	Fetal Brain Male	brain
15	chr4:7695600-7698000	Weak transcription	Fetal Stomach	stomach
16	chr4:7695800-7696800	Enhancers	Fetal Brain Female	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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